.htaccess Settings

I would just send everything to index.php as normal and employ Phalcon's routing to acheive the desired results.

https://docs.phalcon.io/en/latest/reference/routing.html

I see what you are saying...for the API urls that will work. I think the dashboard urls is the real trick right now. I wanted to keep it on the same directory level as the public folder in order to avoid nesting it under public.

You may then want to consider using modules with namespaces https://docs.phalcon.io/en/latest/reference/applications.html#multi-module in your case.

Your structure could then be something like:

app/
    components/
    config/
        config.php
        ...
        ...
        routes.php << Look at the links example but you will be setting routes for each module and declaring defaults
    lib/
    models/
    modules/
        dashboard/
            controllers/
            views/
            Module.php
        api/
            controllers/
            views/
            Module.php   << This is where the magic happens see the link
public/
vendor/

Thanks Andy, that is very close to what I have. I guess if I were to say the question a different way...

Where would the most likely place be for ex a bower_components directory, CSS dir. etc...

I have all of this under /public for the public facing UI...but wanted to avoid the /dashboard under public...

What does "Dashboard" contain?

It would contain a bootstrap/Angular admin area template that I will wire up to Phalcon. So, images/css/JS. The HTML would go in a layouts folder for each module...so ex: dashboard.phtml would be under /apps/modules/backend/layouts/ and populated with views under the backend area